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Crystal Structure of NadE from Streptococcus pyogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris, 20% PEG 4000, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.19 43.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.521 α = 90 b = 93.104 β = 90 c = 128.569 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2014-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 50 92.6 0.123 0.123 12.5 6.6 19874 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 82.9 0.454 2.5 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3hmq 2.5 43.72 18796 1026 93.1 0.17449 0.17165 0.1793 0.22593 0.2314 RANDOM 32.869
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.5 0.79 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.503 r_dihedral_angle_4_deg 25.869 r_dihedral_angle_3_deg 14.267 r_dihedral_angle_1_deg 6.186 r_long_range_B_refined 5.419 r_long_range_B_other 5.052 r_scangle_other 2.242 r_mcangle_it 2.091 r_mcangle_other 2.09 r_scbond_it 1.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.503 r_dihedral_angle_4_deg 25.869 r_dihedral_angle_3_deg 14.267 r_dihedral_angle_1_deg 6.186 r_long_range_B_refined 5.419 r_long_range_B_other 5.052 r_scangle_other 2.242 r_mcangle_it 2.091 r_mcangle_other 2.09 r_scbond_it 1.622 r_angle_refined_deg 1.427 r_scbond_other 1.311 r_mcbond_it 1.192 r_mcbond_other 1.192 r_angle_other_deg 1.139 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4023 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing